Model-based design offers a promising approach for assisting developers to build reliable and secure cyber-physical systems (CPSs) in a systematic manner. In this methodology, a designer first constructs a model, with mathematically precise semantics, of the system under design, and performs extensive analysis with respect to correctness requirements before generating the implementation from the model. However, as new vulnerabilities are discovered, requirements evolve aimed at ensuring resiliency. There is currently a shortage of an inexpensive, automated mechanism that can effectively repair the initial design, and a model-based system developer regularly needs to redesign and reimplement the system from scratch. In this paper, we propose a new methodology along with a Matlab toolkit called REAFFIRM to facilitate the model-based repair for improving the resiliency of CPSs. REAFFIRM takes the inputs including 1) an original hybrid system modeled as a Simulink/Stateflow diagram, 2) a given resiliency pattern specified as a model transformation script, and 3) a safety requirement expressed as a Signal Temporal Logic formula, and then outputs a repaired model which satisfies the requirement. The overall structure of REAFFIRM contains two main modules, a model transformation, and a model synthesizer built on top of the falsification tool Breach. We introduce a new model transformation language for hybrid systems, which we call HATL to allow a designer to specify resiliency patterns. To evaluate the proposed approach, we use REAFFIRM to automatically synthesize repaired models for an adaptive cruise control (ACC) system under a GPS sensor spoofing attack, for a single-machine infinite-bus (SMIB) system under a sliding-mode switching attack, and for a missile guidance system under gyroscopes sensor attack.